Dissecting Phaseolus vulgaris Innate Immune System against Colletotrichum lindemuthianum Infection

Background: The genus Colletotrichum is one of the most economically important plant pathogens, causing anthracnose on a wide range of crops including common beans (Phaseolus vulgaris L.). Crop yield can be dramatically decreased depending on the plant cultivar used and the environmental conditions. This study aimed to identify potential genetic components of the bean immune system to provide environmentally friendly control measures against this fungus. Methodology and Principal Findings: As the common bean is not amenable to reverse genetics to explore functionality and its genome is not fully curated, we used putative Arabidopsis orthologs of bean expressed sequence tag (EST) to perform bioinformatic analysis and experimental validation of gene expression to identify common bean genes regulated during the incompatible interaction with C. lindemuthianum. Similar to model pathosystems, Gene Ontology (GO) analysis indicated that hormone biosynthesis and signaling in common beans seem to be modulated by fungus infection. For instance, cytokinin and ethylene responses were up-regulated and jasmonic acid, gibberellin, and abscisic acid responses were down-regulated, indicating that these hormones may play a central role in this pathosystem. Importantly, we have identified putative bean gene orthologs of Arabidopsis genes involved in the plant immune system. Based on experimental validation of gene expression, we propose that hypersensitive reaction as part of effector-triggered immunity may operate, at least in part, by down-regulating genes, such as FLS2-like and MKK5-like, putative orthologs of the Arabidopsis genes involved in pathogen perception and downstream signaling. Conclusions/Significance: We have identified specific bean genes and uncovered metabolic processes and pathways that may be involved in the immune response against pathogens. Our transcriptome database is a rich resource for mining novel defense-related genes, which enabled us to develop a model of the molecular components of the bean innate immune system regulated upon pathogen attack.

Effect of a rocker non-heeled shoe on EMG and ground reaction forces during gait without previous training

Unstable shoes have been designed to promote "natural instability" and during walking they should simulate barefoot gait, enhancing muscle activity and, thus, attributing an advantage over regular tennis shoes. Recent studies showed that, after special training on the appropriate walking pattern, the use of the Masai Barefoot Technology (MBT) shoe increases muscle activation during walking. Our study presents a comparison of muscle activity as well as horizontal and vertical forces during gait with the MBT, a standard tennis shoe and barefoot walking of healthy individuals without previous training. These variables were compared in 25 female subjects and gait conditions were compared using ANOVA repeated measures (effect size:0.25). Walking with the MBT shoe in this non-instructed condition produced higher vertical forces (first vertical peak and weight acceptance rate) than walking with a standard shoe or walking barefoot, which suggests an increase in the loads received by the musculoskeletal system, especially at heel strike. Walking with the MBT shoe did not increase muscle activity when compared to walking with the standard shoe. The barefoot condition was more effective than the MBT shoe at enhancing muscle activation. Therefore, in healthy individuals, no advantage was found in using the MBT over a standard tennis shoe without a special training period. Further studies using the MBT without any instruction over a longer period are needed to evaluate if the higher loads observed in the present study would return to their baseline values after a period of adaptation, and if the muscle activity would increase over time. (C) 2012 Elsevier B.V. All rights reserved.

Turing patterns in the chlorine dioxide-iodine-malonic acid reaction with square spatial periodic forcing

We use the photosensitive chlorine dioxide-iodine-malonic acid reaction-diffusion system to study wavenumber locking of Turing patterns to two-dimensional "square" spatial forcing, implemented as orthogonal sets of bright bands projected onto the reaction medium. Various resonant structures emerge in a broad range of forcing wavelengths and amplitudes, including square lattices and superlattices, one-dimensional stripe patterns and oblique rectangular patterns. Numerical simulations using a model that incorporates additive two-dimensional spatially periodic forcing reproduce well the experimental observations.

Structure and Ionic Conductivity in the Mixed-Network Former Chalcogenide Glass System [Na2S](2/3)[(B2S3)(x)(P2S5)(1-x)](1/3)

Glasses in the system [Na2S](2/3)[(B2S3)(x)(P2S5)(1-x)](1/3) (0.0 <= x <= 1.0) were prepared by the melt quenching technique, and their properties were characterized by thermal analysis and impedance spectroscopy. Their atomic-level structures were comprehensively characterized by Raman spectroscopy and B-11, P-31, and Na-23 high resolution solid state magic-angle spinning (MAS) NMR techniques. P-31 MAS NMR peak assignments were made by the presence or absence of homonuclear indirect P-31-P-31 spin-spin interactions as detected using homonuclear J-resolved and refocused INADEQUATE techniques. The extent of B-S-P connectivity in the glassy network was quantified by P-31{B-11} and B-11{P-31} rotational echo double resonance spectroscopy. The results clearly illustrate that the network modifier alkali sulfide, Na2S, is not proportionally shared between the two network former components, B and P. Rather, the thiophosphate (P) component tends to attract a larger concentration of network modifier species than predicted by the bulk composition, and this results in the conversion of P2S74-, pyrothiophosphate, Na/P = 2:1, units into PS43-, orthothiophosphate, Na/P = 3:1, groups. Charge balance is maintained by increasing the net degree of polymerization of the thioborate (B) units through the formation of covalent bridging sulfur (BS) units, B S B. Detailed inspection of the B-11 MAS NMR spectra reveals that multiple thioborate units are formed, ranging from neutral BS3/2 groups all the way to the fully depolymerized orthothioborate (BS33-) species. On the basis of these results, a comprehensive and quantitative structural model is developed for these glasses, on the basis of which the compositional trends in the glass transition temperatures (T-g) and ionic conductivities can be rationalized. Up to x = 0.4, the dominant process can be described in a simplified way by the net reaction equation P-1 + B-1 reversible arrow P-0 + B-4, where the superscripts denote the number of BS atoms for the respective network former species. Above x = 0.4, all of the thiophosphate units are of the P-0 type and both pyro-(B-1) and orthothioborate (B-0) species make increasing contributions to the network structure with increasing x. In sharp contrast to the situation in sodium borophosphate glasses, four-coordinated thioborate species are generally less abundant and heteroatomic B-S-P linkages appear to not exist. On the basis of this structural information, compositional trends in the ionic conductivities are discussed in relation to the nature of the charge-compensating anionic species and the spatial distribution of the charge carriers.

Long-term amphetamine treatment exacerbates inflammatory lung reaction while decreases airway hyper-responsiveness after allergic stimulus in rats

Asthma is an allergic lung disease can be modulated by drugs that modify the activity of central nervous system (CNS) such as amphetamine (AMPH). AMPH is a highly abused drug that exerts potent effects on behavior and immunity. In this study we investigated the mechanism involved in the effects of long-term AMPH treatment on the increased magnitude of allergic lung response. We evaluated mast cells degranulation, cytokines release, airways responsiveness and, expression of adhesion molecules. Male Wistar rats were treated with AMPH or vehicle (PBS) for 21 days and sensitized with ovalbumin (OVA) one week after the first injection of vehicle or AMPH. Fourteen days after the sensitization, the rats were challenged with an OVA aerosol, and 24 h later their parameters were analyzed. In allergic rats, the treatment with AMPH exacerbated the lung cell recruitment due increased expression of ICAM-1, PECAM-1 and Mac-1 in granulocytes and macrophages recovered from bronchoalveolar lavage. Elevated levels of IL-4, but decreased levels of IL-10 were also found in samples of lung explants after AMPH treatment. Conversely, the ex-vivo tracheal hyper-responsiveness to methacholine (MCh) was reduced by AMPH treatment, whereas the force contraction of tracheal segments due to in vitro antigen challenge remained unaltered. Our findings suggest that lung inflammation and airway hyper-responsiveness due to OVA challenge are under the distinct control of AMPH during long-term treatment. Our data strongly indicate that AMPH positively modulates allergic lung inflammation via the increase of ICAM-1, PECAM-1, Mac-1 and IL-4. AMPH also abrogates the release of the anti-inflammatory cytokine IL-10. (c) 2012 Elsevier B.V. All rights reserved.

Behavioral characterization of the alarm reaction and anxiolytic-like effect of acute treatment with fluoxetine in piaucu fish

In Ostariophysan fish, the detection of the alarm substance liberated into the water as a consequence of an attack by a predator elicits an alarm reaction or anti-predatory behavior. In this study, experiments were performed to: (i) describe and quantitatively characterize the behavioral and ventilatory responses in piaucu fish (Leporinus macrocephalus), individually and as part of a school, to conspecific alarm substance (CAS) and; (ii) test the effect of acute fluoxetine treatment on alarm reaction. Histological analysis revealed the presence of club cells in the intermediate and superficial layers of the epidermis. The predominant behavioral response to CAS was freezing for fish held individually, characterized by the cessation of the swimming activity as the animal settles to a bottom corner of the aquarium. Fish exposed to CAS showed decrease in the mean ventilatory frequency (approximately 13%) relative to control. In schools, CAS elicited a biphasic response that was characterized by erratic movements followed by increased school cohesion and immobility, reflected as an increased school cohesion (65.5% vs. -5.8% for controls) and in the number of animals near the bottom of the aquarium (42.0% vs. 6.5% for controls). Animals treated with single i.p. injections of fluoxetine (10 mu g/g b.w.) did not exhibit alarm behavior following CAS stimulation. These results show that an alarm pheromone system is present in piaucu fish, evidenced by the presence of epidermal club cells and an alarm reaction induced by CAS and consequently of a chemosensory system to transmit the appropriate information to neural structures responsible for initiating anti-predator behavioral responses. In addition, fluoxetine treatment caused an anxiolytic-like effect following CAS exposure. Thus, the alarm reaction in piaucu can be a useful model for neuroethological and pharmacological studies of anxiety-related states. (C) 2011 Elsevier Inc. All rights reserved.

Quantification of Short and Medium Range Order in Mixed Network Former Glasses of the System GeO2-NaPO3: A Combined NMR and X-ray Photoelectron Spectroscopy Study

Glasses in the system xGeO(2)-(1-x)NaPO3 (0 <= x <= 0.50) were prepared by conventional melting quenching and characterized by thermal analysis, Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and P-31 nuclear magnetic resonance (MAS NMR) techniques. The deconvolution of the latter spectra was aided by homonuclear J-resolved and refocused INADEQUATE techniques. The combined analyses of P-31 MAS NMR and O-1s XPS lineshapes, taking charge and mass balance considerations into account, yield the detailed quantitative speciations of the phosphorus, germanium, and oxygen atoms and their respective connectivities. An internally consistent description is possible without invoking the formation of higher-coordinated germanium species in these glasses, in agreement with experimental evidence in the literature. The structure can be regarded, to a first approximation, as a network consisting of P-(2) and P-(3) tetrahedra linked via four-coordinate germanium. As implied by the appearance of P-(3) units, there is a moderate extent of network modifier sharing between phosphate and germanate network formers, as expressed by the formal melt reaction P-(2) + Ge-(4) -> P-(3) + Ge-(3). The equilibrium constant of this reaction is estimated as K = 0.52 +/- 0.11, indicating a preferential attraction of network modifier by the phosphorus component. These conclusions are qualitatively supported by Raman spectroscopy as well as P-31{Na-23} and P-31{Na-23} rotational echo double resonance (REDOR) NMR results. The combined interpretation of O-1s XPS and P-31 MAS NMR spectra shows further that there are clear deviations from a random connectivity scenario: heteroatomic P-O-Ge linkages are favored over homoatomic P-O-P and Ge-O-Ge linkages.

Novel cross-coupling reactions between organotellurides and Grignard reagents employing a MnCl2/CuI catalytic system

We present a general protocol for the cross-coupling reaction of Grignard reagents and organic tellurides. Aryl Grignard reagents react stereospecifically with vinyl tellurides in the presence of a catalytic amount of manganese (II) chloride and copper (I) iodide to produce good yields of the corresponding cross-coupling products. (C) 2012 Published by Elsevier Ltd.

Study of CuO/CeO2 catalyst with for preferential CO oxidation reaction in hydrogen-rich feed (PROX-CO)

The CuO/CeO2 system was investigated as a catalyst for preferential CO oxidation reaction in hydrogen-rich feed (PROX-CO). The catalysts were prepared by deposition-precipitation (DEP) and co-precipitation (COP) methods and the catalytic performance reveals that the preparation method influences the properties of solids prepared, where a direct consequence is the difference in behavior of the catalysts in the PROX-CO reaction. A high specific area and a better dispersion of the metallic phase were obtained in the catalyst prepared by co-precipitation. The redox properties during the reaction were reported by measures of temperature programmed reduction (TPR), OSC measurements and X-ray absorption near edge structure (XANES-TPR) in situ showed the relationship between the preparation method, the physicochemical characteristics and redox properties in the PROX-CO reaction. By this means, the good dispersion of CuO and the best oxygen capacity are the response of the high performance of CuO/CeO2-COP catalysts for the PROX-CO reaction. Crown Copyright (c) 2012 Published by Elsevier B.V. All rights reserved.

Photobiological effect of low-level laser irradiation in bovine embryo production system

The objectives of this study were to evaluate the effect of low-level laser irradiation (LLLI) on bovine oocyte and granulosa cells metabolism during in vitro maturation (IVM) and further embryo development. Cumulus-oocytes complexes (COCs) were subjected (experimental group) or not (control group) to irradiation with LLLI in a 633-nm wavelength and 1 J/cm2 fluency. The COCs were evaluated after 30 min, 8, 16, and 24 h of IVM. Cumulus cells were evaluated for cell cycle status, mitochondrial activity, and viability (flow cytometry). Oocytes were assessed for meiotic progression status (nuclear staining), cell cycle genes content [real-time polymerase chain reaction (PCR)], and signal transduction status (western blot). The COCs were also in vitro fertilized, and the cleavage and blastocyst rates were assessed. Comparisons among groups were statistically performed with 5% significance level. For cumulus cells, a significant increase in mitochondrial membrane potential and the number of cells progressing through the cycle could be observed. Significant increases on cyclin B and cyclin-dependent kinase (CDK4) levels were also observed. Concerning the oocytes, a significantly higher amount of total mitogen-activated protein kinase was found after 8 h of irradiation, followed by a decrease in all cell cycle genes transcripts, exception made for the CDK4. However, no differences were observed in meiotic progression or embryo production. In conclusion, LLLI is an efficient tool to modulate the granulosa cells and oocyte metabolism

The photosynthetic bacterial reaction center in native and artificial envirnoments: effects on light-induced electron transfer

In this thesis we focussed on the characterization of the reaction center (RC) protein purified from the photosynthetic bacterium Rhodobacter sphaeroides. In particular, we discussed the effects of native and artificial environment on the light-induced electron transfer processes. The native environment consist of the inner antenna LH1 complex that copurifies with the RC forming the so called core complex, and the lipid phase tightly associated with it. In parallel, we analyzed the role of saccharidic glassy matrices on the interplay between electron transfer processes and internal protein dynamics. As a different artificial matrix, we incorporated the RC protein in a layer-by-layer structure with a twofold aim: to check the behaviour of the protein in such an unusual environment and to test the response of the system to herbicides. By examining the RC in its native environment, we found that the light-induced charge separated state P+QB - is markedly stabilized (by about 40 meV) in the core complex as compared to the RC-only system over a physiological pH range. We also verified that, as compared to the average composition of the membrane, the core complex copurifies with a tightly bound lipid complement of about 90 phospholipid molecules per RC, which is strongly enriched in cardiolipin. In parallel, a large ubiquinone pool was found in association with the core complex, giving rise to a quinone concentration about ten times larger than the average one in the membrane. Moreover, this quinone pool is fully functional, i.e. it is promptly available at the QB site during multiple turnover excitation of the RC. The latter two observations suggest important heterogeneities and anisotropies in the native membranes which can in principle account for the stabilization of the charge separated state in the core complex. The thermodynamic and kinetic parameters obtained in the RC-LH1 complex are very close to those measured in intact membranes, indicating that the electron transfer properties of the RC in vivo are essentially determined by its local environment. The studies performed by incorporating the RC into saccharidic matrices evidenced the relevance of solvent-protein interactions and dynamical coupling in determining the kinetics of electron transfer processes. The usual approach when studying the interplay between internal motions and protein function consists in freezing the degrees of freedom of the protein at cryogenic temperature. We proved that the “trehalose approach” offers distinct advantages with respect to this traditional methodology. We showed, in fact, that the RC conformational dynamics, coupled to specific electron transfer processes, can be modulated by varying the hydration level of the trehalose matrix at room temperature, thus allowing to disentangle solvent from temperature effects. The comparison between different saccharidic matrices has revealed that the structural and dynamical protein-matrix coupling depends strongly upon the sugar. The analyses performed in RCs embedded in polyelectrolyte multilayers (PEM) structures have shown that the electron transfer from QA - to QB, a conformationally gated process extremely sensitive to the RC environment, can be strongly modulated by the hydration level of the matrix, confirming analogous results obtained for this electron transfer reaction in sugar matrices. We found that PEM-RCs are a very stable system, particularly suitable to study the thermodynamics and kinetics of herbicide binding to the QB site. These features make PEM-RC structures quite promising in the development of herbicide biosensors. The studies discussed in the present thesis have shown that, although the effects on electron transfer induced by the native and artificial environments tested are markedly different, they can be described on the basis of a common kinetic model which takes into account the static conformational heterogeneity of the RC and the interconversion between conformational substates. Interestingly, the same distribution of rate constants (i.e. a Gamma distribution function) can describe charge recombination processes in solutions of purified RC, in RC-LH1 complexes, in wet and dry RC-PEM structures and in glassy saccharidic matrices over a wide range of hydration levels. In conclusion, the results obtained for RCs in different physico-chemical environments emphasize the relevance of the structure/dynamics solvent/protein coupling in determining the energetics and the kinetics of electron transfer processes in a membrane protein complex.

Synthetic and mechanistic investigation of new radical processes: reaction of organic azides with group-XIII Lewis acids

Dichloroindium hydride revealed to be a valid alternative to tributyltin hydride for radical reduction of organic (alkyl, aryl, acyl, solfonyl) azides. The new approach entails mild reaction conditions and provides high yields of the corresponding amines and amides, also showing high degrees of selectivity. The system dichloroindium hydride / azides can be utilised in fivemembered ring closures of g-azidonitriles, as a new source of aminyl radicals for the attractive synthesis of interesting amidine compounds in the absence of both toxic reagents and tedious purification procedures. Allylindium dichloride seems a good substitute for dichloroindium hydride for generation of indium centred radicals under photolytic conditions, since it allows allylation of electrophilic azides (e.g. phenylsulfonyl azide) and halogen or ester δ-substituted azides, the latter through a 1,5-H transfer rearrangement mechanism. Evidences of the radical nature of the reactions mechanism were provided by ESR spectroscopy, furthermore the same technique, allowed to discover that the reaction of azides with indium trichloride and other group XIII Lewis acids, in particular gallium trichloride, gives rise to strongly coloured, persistent paramagnetic species, whose structure is consistent with the radical cation of the head-to-tail dimer of the aniline corresponding to the starting azide.

Microwave-Mediated Hetero Diels-Alder reaction: Synthesis of biologically active compounds

Heterocyclic compounds represent almost two-thirds of all the known organic compounds: they are widely distributed in nature and play a key role in a huge number of biologically important molecules including some of the most significant for human beings. A powerful tool for the synthesis of such compounds is the hetero Diels-Alder reaction (HDA), that involve a [4+2] cycloaddition reaction between heterodienes and suitable dienophiles. Among heterodienes to be used in such six-membered heterocyclic construction strategy, 3-trialkylsilyloxy-2-aza-1,3-dienes (Fig 1) has been demonstrated particularly attractive. In this thesis work, HDA reactions between 2-azadienes and carbonylic and/or olefinic dienophiles, are described. Moreover, substitution of conventional heating by the corresponding dielectric heating as been explored in the frame of Microwave-Assisted-Organic-Synthesis (MAOS) which constitutes an up-to-grade research field of great interest both from an academic and industrial point of view. Reaction of the azadiene 1 (Fig 1) will be described using as dienophiles carbonyl compounds as aldehyde and ketones. The six-membered adducts thus obtained (Scheme 1) have been elaborated to biologically active compounds like 1,3-aminols which constitutes the scaffold for a wide range of drugs (Prozac®, Duloxetine, Venlafaxine) with large applications in the treatment of severe diseases of nervous central system (NCS). Scheme 1 The reaction provides the formation of three new stereogenic centres (C-2; C-5; C-6). The diastereoselective outcome of these reactions has been deeply investigated by the use of various combination of achiral and chiral azadienes and aliphatic, aromatic or heteroaromatic aldehydes. The same approach, basically, has been used in the synthesis of piperidin-2-one scaffold substituting the carbonyl dienophile with an electron poor olefin. Scheme 2 As a matter of fact, this scaffold is present in a very large number of natural substances and, more interesting, is a required scaffold for an huge variety of biologically active compounds. Activated olefins bearing one or two sulfone groups, were choose as dienophiles both for the intrinsic characteristic flexibility of the “sulfone group” which may be easily removed or elaborated to more complex decorations of the heterocyclic ring, and for the electron poor property of this dienophiles which makes the resulting HDA reaction of the type “normal electron demand”. Synthesis of natural compounds like racemic (±)-Anabasine (alkaloid of Tobacco’s leaves) and (R)- and (S)-Conhydrine (alkaloid of Conium Maculatum’s seeds and leaves) and its congeners, are described (Fig 2).

The topological trigger system of the TOF detector for the ALICE experiment at the LHC

The ALICE experiment at the LHC has been designed to cope with the experimental conditions and observables of a Quark Gluon Plasma reaction. One of the main assets of the ALICE experiment with respect to the other LHC experiments is the particle identification. The large Time-Of-Flight (TOF) detector is the main particle identification detector of the ALICE experiment. The overall time resolution, better that 80 ps, allows the particle identification over a large momentum range (up to 2.5 GeV/c for pi/K and 4 GeV/c for K/p). The TOF makes use of the Multi-gap Resistive Plate Chamber (MRPC), a detector with high efficiency, fast response and intrinsic time resoltion better than 40 ps. The TOF detector embeds a highly-segmented trigger system that exploits the fast rise time and the relatively low noise of the MRPC strips, in order to identify several event topologies. This work aims to provide detailed description of the TOF trigger system. The results achieved in the 2009 cosmic-ray run at CERN are presented to show the performances and readiness of TOF trigger system. The proposed trigger configuration for the proton-proton and Pb-Pb beams are detailed as well with estimates of the efficiencies and purity samples.

Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.